Alignments for a candidate for asp-kinase in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for asp-kinase in Pseudomonas simiae WCS417

Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF4227 PS417_21655 aspartate kinase

Query= SwissProt::C3JXY0
         (413 letters)



>FitnessBrowser__WCS417:GFF4227
          Length = 413

 Score =  786 bits (2029), Expect = 0.0
 Identities = 413/413 (100%), Positives = 413/413 (100%)

Query: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60
           MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD
Sbjct: 1   MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAKAISGD 60

Query: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120
           QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD
Sbjct: 61  QQPLPRELDVIVSTGEQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD 120

Query: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180
           QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV
Sbjct: 121 QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 180

Query: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240
           YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT
Sbjct: 181 YTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFKEGPGT 240

Query: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300
           LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV
Sbjct: 241 LITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISGANIEVDMIVQNV 300

Query: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360
           SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS
Sbjct: 301 SHDNTTDFTFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVAS 360

Query: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413
           RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE
Sbjct: 361 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDAPARQGE 413


Lambda     K      H
   0.316    0.133    0.357 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 739
Number of extensions: 23
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 413
Length of database: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate GFF4227 PS417_21655 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00656.hmm
# target sequence database:        /tmp/gapView.2972266.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00656  [M=407]
Accession:   TIGR00656
Description: asp_kin_monofn: aspartate kinase, monofunctional class
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.7e-136  441.4  13.1   1.9e-136  441.2  13.1    1.0  1  FitnessBrowser__WCS417:GFF4227  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF4227  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.2  13.1  1.9e-136  1.9e-136       1     406 [.       1     405 [.       1     406 [. 0.97

  Alignments for each domain:
  == domain 1  score: 441.2 bits;  conditional E-value: 1.9e-136
                       TIGR00656   1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerdelvsvG 79 
                                     + liVqKFGGtsvgs+eri+++a++v+k    g++ vVV+SAms++t++l++la+    + +  +++ pre d +vs+G
  FitnessBrowser__WCS417:GFF4227   1 MALIVQKFGGTSVGSVERIEQVADKVKKFRDAGDDLVVVLSAMSGETNRLIDLAK----AISGDQQPLPRELDVIVSTG 75 
                                     579***************************************************4....334456789*********** PP

                       TIGR00656  80 EllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGateeGeiTtLGRG 158
                                     E++++all++al+++gv a++++g +  ilTd+ +++A+i +++  +++   L+ g +vvvaGF+G +e+G+iTtLGRG
  FitnessBrowser__WCS417:GFF4227  76 EQVTIALLAMALNKRGVPAVSYTGSQVRILTDSAHTKARILQIDD-QKIRTDLKAGRVVVVAGFQGVDEQGNITTLGRG 153
                                     ********************************************9.9******************************** PP

                       TIGR00656 159 GSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlhpralelaveakvpilvrs 237
                                     GSD+t ++laaalkAd+++iyTDV+GvyttDPrvv+ a+++dki++eE+le+A+lG kvl+ ra+e+a +++vp++v +
  FitnessBrowser__WCS417:GFF4227 154 GSDTTGVALAAALKADECQIYTDVDGVYTTDPRVVSVAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLH 232
                                     ******************************************************************************* PP

                       TIGR00656 238 skekeegTlitn....kkensslvkaialeknvarltvegegmlgkrgilaeifkaLaeeeinvdlisqtese...tsi 309
                                     s+++  gTlit     ++e++ ++++ia++++ a+lt++  g+ + +g++ +i + ++ ++i vd+i+q  s+   t+ 
  FitnessBrowser__WCS417:GFF4227 233 SFKEGPGTLITIdeeeSMEQP-IISGIAFNRDEAKLTIR--GVPDTPGVAFKILGPISGANIEVDMIVQNVSHdntTDF 308
                                     **********98555566666.*****************..9****************************9988999** PP

                       TIGR00656 310 slvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlv 388
                                     +++v++++ d+a+++L+++ ++++ +++  + ++a+vsivg+g++++ Gvas++f+al+++ ini mis+se+k+sv++
  FitnessBrowser__WCS417:GFF4227 309 TFTVHRNEYDAAERILQNTAKEIGAREVVGDTKIAKVSIVGVGMRSHAGVASRMFEALAKESINIQMISTSEIKVSVVI 387
                                     ******************************************************************************* PP

                       TIGR00656 389 dekdaekavrklheklee 406
                                     +ek++e avr+lh ++e+
  FitnessBrowser__WCS417:GFF4227 388 EEKYLELAVRALHTAFEL 405
                                     ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (407 nodes)
Target sequences:                          1  (413 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 21.85
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis